Odenthal-Hesse, L.; Dutheil, J. Y.; Klötzl, F.; Haubold, B.: hotspot: software to support sperm-typing for investigating recombination hotspots. Bioinformatics 32 (16), pp. 2554 - 2555 (2016)

Dutheil, J. Y.: Hidden Markov models in population genomics. In: Hidden Markov Models: Methods and Protocols, pp. 149 - 164 (Eds. Westhead, D. R.; Vijayabaskar, M. S.). Springer Science+Business Media LLC, New York (2017)

Liang, J.: Population genomic inference with the ancestral recombination graph (ARG): recombination landscape and ancestral state reconstruction. Dissertation, V, 128 pp., Christian-Albrechts-Universität, Kiel (2025)

Puzović, N.: Living with noise: The evolution of gene expression noise in gene regulatory networks. Dissertation, 146 pp., Christian Albrechts University of Kiel, Kiel; Plön (2023)

Haider, M. B.: Compensatory evolution within proteins: An experimental assessment. Dissertation, 155 pp., Christian-Albrechts-Universität, Kiel (2021)

Kadib Alban, A. S.: The magnitude of DNA transfer between plasmids and chromosomes in Prokaryotes. Dissertation, Christian-Albrechts-Universität, Kiel (2021)

Moutinho, A. F.: Unravelling the determinants of the rate of adaptive evolution at the molecular level. Dissertation, 168 pp., Faculty of Mathematics and Natural Sciences, Christian Albrechts University of Kiel, Kiel (2020)

Barroso, G.: Darwin throws dice: modelling stochastic processes of molecular evolution. Dissertation, 156 pp., Christian-Albrechts-Universität, Kiel (2019)

Hamidi, D.: Computational insights into the reproduction strategies of Saccharomyces cerevisiae populations: inferring recombination and selfing rates through sequentially Markovian coalescent models. Master, 72 pp., Christian-Albrechts-Universität, Kiel (2024)

Joffroy, K.: Squamata phylogenomics and molecular evolution of venom proteins in Toxicofera. Master, 77 pp., Christian-Albrechts-Universität, Kiel (2022)

Trancoso, F. F.: Inferring transcriptional noise in Saccharomyces paradoxus using high-throughput single-cell transcriptomics. Master, 62 pp., Christian-Albrechts-Universität, Kiel (2022)

Raas, M. W. D.: The impact of domestication on the rate of adaptive evolution in yeast. Master, Radboud University, Faculty of Medical Sciences, Nijmegen, The Netherlands (2021)

Le Veve, A.; İltaş, Ö.; Dutheil, J. Y.; Placette, C. L.: The paternally expressed genes in endosperm comfort the kinship theory to explain imprinting in A. lyrata. (2025)

Liang, J.; Dutheil, J. Y.: Polarizing SNPs without outgroup. (2025)

Puzović, N.; Dutheil, J. Y.: When is gene expression noise advantageous? (2023)